Hello everyone,<br> Thanks to Justin Lemkul and Thomas Schlesier for replying to my question in vol. 65 issues 96 and 98.<br> I am trying to convert a pdb file to a gro file using pdb2gmx -f waters.pdb -o waters.gro and I get the message:<br>
<br>Select the Force Field:<br> 0: GROMOS96 43a1 force field <br> 1: GROMOS96 43a2 force field (improved alkane dihedrals)<br> 2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)<br> 3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) <br>
4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) <br> 5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)<br> 6: [DEPRECATED] Gromacs force field (see manual)<br> 7: [DEPRECATED] Gromacs force field with hydrogens for NMR<br>
8: Encad all-atom force field, using scaled-down vacuum charges<br> 9: Encad all-atom force field, using full solvent charges <br><br>I don't want to use any of these force fields. I want to use the charmm27 one. How do I select that? Do I need to modify the code? If so, where do I find it? <br>
Also, I read in a Spidertoxin tutorial that editconf can be used to convert a .pdb file to a .gro file. I tried this but error message says: "No velocities found." I know that pdb files generally do not have velocities and these velocities can be generated by setting genvel=yes in the mdp file. How can a .pdb file contain initial velocities?<br>
<br>Thank you,<br>Lum<br>